1. Field of the Invention
This invention resides in the field of laboratory equipment used in performing simultaneous assays on a multitude of species or reaction media in individual spots on a microscope slide or in individual wells of a microtiter plate or multi-well plates in general that are designed for performing large numbers of simultaneous small-volume assays. In particular, this invention addresses issues that arise when assays on these slides or plates are read or monitored by optical scanning.
2. Description of the Prior Art
Multi-well plates of many sizes, including the standard microtiter plate with 96 wells in a 12×8 array and a spacing of 9 mm between wells, as well as plates with as few as six or as many as several thousand wells, are widely used in biochemical laboratories. Large numbers of small samples are assayed simultaneously on these plates by automated instrumentation for purposes such as screening, determining binding affinities or other structural characteristics, or otherwise characterizing the samples. Glass slides with two-dimensional arrays of spots or microdots printed on their surfaces are used in an analogous fashion, the spots or microdots containing even smaller samples. The species analyzed on these wells and spots are often biological species such as proteins, peptide sequences, or nucleic acid fragments. Plates and slides of these types are also used for testing small molecule libraries synthesized by chemical laboratories and supplied to researchers for studies in cheminformatics and bioinformatics, where molecules in the libraries are screened for chemical or biological activity such as gene function and target binding.
Optical scanning is a highly effective means of detection for assays performed on these plates and slides, since optical scanner heads can rapidly traverse the entire array while focusing on individual wells or spots in succession and performing all of the functions of detection at each site. Optical data is also readily stored, quantified, and processed by automated instrumentation. To achieve high performance with large arrays of small wells or spots, the most effective optical scanning systems are those that have limited depth of field. Limited field depths and limited field detection systems are more effective in rejecting background fluorescence than are systems with a large field of view and depth of focus.                Optical scanning systems typically use confocal optics with a depth of field of about 1 to 10 microns. Accurate detection with such a short depth of field requires a high degree of uniformity of the spacing between each sample and the scanner head optical system.        
To achieve close tolerance with such a short depth of field, many multi-well plates are constructed with flat bottoms of glass or other transparent material to allow scanning to be performed through the bottom of the plate. This is particularly effective when the solvents and other suspending media have been removed from the wells and the reaction species are deposited in a layer on the floor of each well. Even when scanning is performed through the bottom plate, however, the plate must be held in a level position with all areas of the bottom plate at the same distance from the travel plane of the scanning head to achieve accurate and uniform scanning. Minute defects in the plate such as variations in the thickness of the transparent bottom and warpage of the plate can cause this distance to vary from one site on the plate to the next and thereby interfere with the scanning accuracy. Similar variations occur in glass slides, where the thickness of the typical slide can vary by 50 microns or more.